Error when running ms2pip in the linux terminal

[MarcIsak]

Hi,

I tried to process a batch of .peprec files in ms2pip (those that Ralf generated for me in issue #61), to create predicted output files in spectronaut.csv format instead of just csv. I noticed that quite a few peprec files, precursors_split(00, 03, 04, 07, 08, 09, 11, 16, 17, 18).peprec_, generated the following error when being processed with ms2pip:

_--- Logging error ---
Traceback (most recent call last):
File "/usr/lib/python3.8/logging/init.py", line 1081, in emit
msg = self.format(record)
File "/usr/lib/python3.8/logging/init.py", line 925, in format
return fmt.format(record)
File "/usr/lib/python3.8/logging/init.py", line 664, in format
record.message = record.getMessage()
File "/usr/lib/python3.8/logging/init.py", line 369, in getMessage
msg = msg % self.args
TypeError: not all arguments converted during string formatting
Call stack:
File "/home/marc/PycharmProjects/MS2PIP/venv/bin/ms2pip", line 8, in
sys.exit(main())
File "/home/marc/PycharmProjects/MS2PIP/venv/lib/python3.8/site-packages/ms2pip/main.py", line 123, in main
ms2pip.run()
File "/home/marc/PycharmProjects/MS2PIP/venv/lib/python3.8/site-packages/ms2pip/ms2pipC.py", line 759, in run
self._read_peptide_information()
File "/home/marc/PycharmProjects/MS2PIP/venv/lib/python3.8/site-packages/ms2pip/ms2pipC.py", line 842, in read_peptide_information
logger.info(
Message: 'Removed {} unsupported peptide sequences (< 3, > 99 amino acids, or containing B, J, O, U, X or Z).'
Arguments: (11,)

I think that the message in this error is strange as all peptide sequences are between 7 and 50 AA, and they should not have any of the AAs: B, J, O, U, X or Z.

Any ideas? The peprec files can be found in issue #61

Best,

Marc

[RalfG]

Hi Marc,
I checked the file with the precursors, and there are in fact peptides with B, Z and X amino acids. There does occur a bug while writing this error message, but that shouldn't influence the results. Does the script continue to run after this error message?